Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. Strugatskii

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Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. Strugatskii. / Konstantinov, Dmitrii K.; Menzorov, Aleksei; Krivenko, Olga et al.

In: PeerJ, Vol. 10, e12737, 03.2022.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{f8c47f98006e4d238ef68281eb1fae63,

title = "Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. Strugatskii",

abstract = "Background. Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods. We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results. The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion. Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.",

keywords = "Fatty acids, Marine protists, RNA-seq, Thraustochytrium, Transcriptome assembly",

author = "Konstantinov, {Dmitrii K.} and Aleksei Menzorov and Olga Krivenko and Doroshkov, {Alexey V.}",

note = "Funding Information: The study was supported by the Ministry of Education and Science of the Russian Federation, grant 2019-0546 (FSUS-2020-0040). Part of the work carried out by O.V. Krivenko was done at the Laboratory of Marine Biodiversity and Functional Genomics (created with the support of grant No. 14.W03.31.0015), and was funded by IBSS GA No. 121030100028-0. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funding Information: The following grant information was disclosed by the authors: The Ministry of Education and Science of the Russian Federation, grant 2019-0546: FSUS-2020-0040. The Laboratory of Marine Biodiversity and Functional Genomics: 14.W03.31.0015. IBSS GA: 121030100028-0. Publisher Copyright: {\textcopyright} 2022 Konstantinov et al.",

year = "2022",

month = mar,

doi = "10.7717/peerj.12737",

language = "English",

volume = "10",

journal = "PeerJ",

issn = "2167-8359",

publisher = "PeerJ",

}

RIS

TY - JOUR

T1 - Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. Strugatskii

AU - Konstantinov, Dmitrii K.

AU - Menzorov, Aleksei

AU - Krivenko, Olga

AU - Doroshkov, Alexey V.

N1 - Funding Information: The study was supported by the Ministry of Education and Science of the Russian Federation, grant 2019-0546 (FSUS-2020-0040). Part of the work carried out by O.V. Krivenko was done at the Laboratory of Marine Biodiversity and Functional Genomics (created with the support of grant No. 14.W03.31.0015), and was funded by IBSS GA No. 121030100028-0. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funding Information: The following grant information was disclosed by the authors: The Ministry of Education and Science of the Russian Federation, grant 2019-0546: FSUS-2020-0040. The Laboratory of Marine Biodiversity and Functional Genomics: 14.W03.31.0015. IBSS GA: 121030100028-0. Publisher Copyright: © 2022 Konstantinov et al.

PY - 2022/3

Y1 - 2022/3

N2 - Background. Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods. We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results. The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion. Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.

AB - Background. Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. Methods. We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore Beroe ovata using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. Results. The protist belongs to the genus Thraustochytrium based on the 18S rRNA sequence analysis. We designated the isolated protist as T. aureum ssp. strugatskii. The closest species with the genome assembly is Schizochytrium aggregatum. Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Conclusion. Our findings suggest that the T. aureum ssp. strugatskii is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.

KW - Fatty acids

KW - Marine protists

KW - RNA-seq

KW - Thraustochytrium

KW - Transcriptome assembly

UR - http://www.scopus.com/inward/record.url?scp=85126270624&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/26f25f7b-bde8-3f3c-ad7b-61bf262ada4c/

U2 - 10.7717/peerj.12737

DO - 10.7717/peerj.12737

M3 - Article

C2 - 35287351

AN - SCOPUS:85126270624

VL - 10

JO - PeerJ

JF - PeerJ

SN - 2167-8359

M1 - e12737

ER -

ID: 35705409